Timp and his team have already developed new computational software that determines whether a human DNA sample includes an epigenetic add-on linked to cancer and other adverse health conditions.

Using nanopore sequencing, Timp is able to read a variety of DNA marks that tell cells which genes to express and what bodily “programs” to run. In a situation where cells develop a disease such as cancer, these marks can become distorted.

Sequencing of these epigenetic marks can be logistically difficult and limited with current technologies, resulting in harsh handling of the DNA sample and the need to use particularly large and pre-treated tissue samples.

With this grant, Timp and his team will work to develop a method to better read the methylation information that is encoded in the DNA sequence. Methylation refers to the presence of a biochemical group attached to a nucleotide, the genetic building blocks that make up DNA.

“Nanopore sequencing reads the DNA sequence, and the methylation information comes along for free. It’s encoded in the data,” explains Timp. “We’re trying to determine how to pull it out.”

The new software Timp helped develop will be used with a commercially available nanopore sequencing device. This technique can directly characterize DNA methylation from smaller tissue samples.

In the Feb. 20 issue of the journal Nature Methods, Timp and team members from Johns Hopkins University, the Ontario Institute for Cancer Research, and the University of Toronto for the first time detailed their new method of detecting the presence of an extra mark on DNA.

NHGRI is one of the 27 institutes and centers at the National Institutes of Health. The Research Project Grant (R01) provides support for health-related research and development based on the mission of the NIH.